title: Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato.
abstract: Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
authors.affiliation: Department of Plant Biology, University of California, Davis, CA 95616, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Koenig
authors.forename: José M
authors.initials: JM
authors.lastname: Jiménez-Gómez
authors.forename: Seisuke
authors.initials: S
authors.lastname: Kimura
authors.forename: Daniel
authors.initials: D
authors.lastname: Fulop
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Chitwood
authors.forename: Lauren R
authors.initials: LR
authors.lastname: Headland
authors.forename: Ravi
authors.initials: R
authors.lastname: Kumar
authors.forename: Michael F
authors.initials: MF
authors.lastname: Covington
authors.forename: Upendra Kumar
authors.initials: UK
authors.lastname: Devisetty
authors.forename: An V
authors.initials: AV
authors.lastname: Tat
authors.forename: Takayuki
authors.initials: T
authors.lastname: Tohge
authors.forename: Anthony
authors.initials: A
authors.lastname: Bolger
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
authors.forename: Stephan
authors.initials: S
authors.lastname: Ossowski
authors.forename: Christa
authors.initials: C
authors.lastname: Lanz
authors.forename: Guangyan
authors.initials: G
authors.lastname: Xiong
authors.forename: Mallorie
authors.initials: M
authors.lastname: Taylor-Teeples
authors.forename: Siobhan M
authors.initials: SM
authors.lastname: Brady
authors.forename: Markus
authors.initials: M
authors.lastname: Pauly
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Björn
authors.initials: B
authors.lastname: Usadel
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.forename: Jie
authors.initials: J
authors.lastname: Peng
authors.forename: Neelima R
authors.initials: NR
authors.lastname: Sinha
authors.forename: Julin N
authors.initials: JN
authors.lastname: Maloof
mesh_terms: D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D012641:Selection, Genetic; D059467:Transcriptome
keywords: abiotic stress; biotic stress; domestication